Before you start delving into the (potentially, at least) murky waters of re-installing software, why not try to establish what the fault actually is, or is likely to be.
Assuming that the system worked OK before (and you have seen it working) ... what has happened to upset it since? Has there been an interruption of mains power recently, for example?
And, what messages do those error pop-ups convey?
Who knows; the problem could be something at the Console Advance end ... or even (lack of) communication between the Console and the Plate Reader (XG5000).
Meanwhile, the service manual for the earlier FCR 5000 version is available on line. Unusually for modern manuals, it is quite detailed (23 Meg .pdf). It was revised in 2005, but I'm not sure it would be any use for the XG5000.